Re: Butchering:
My final solution will be to tie two males (In case of death due to old age) and around 20-25 females for each species to ropes and butcher the newborns immediately after birth. Yea, you get less bones/meat/fat, but a) the design is simple as hell, b) the only thing the bone count affects is the number of bone bolts produced, and I already have an enormous stockpile (Currently around 6400 bone bolts stockpiled), c) the loss of a couple meat per stack is unimportant (Most of my cooked food ends up rotting in the kitchens anyways as I'm mainly training my cooks at the moment) and d) it may actually result in *more* total meat/bones being produced due to the fact that you can be near the animal pop cap and have constant births from every potential mother.
My three butchers have a combined experience total of 23k xp in butchery (11, 9, 3). Hell, I even recently turned off food hauling for the primary butcher in order to get through the backlog. Note that I have two butcher shops that are working almost around the clock and that third butcher was only added fairly recently. In general, my "Butcher" dwarves only have butchering, tanning, leather working, and food hauling enabled. The recent addition, however, has leather working disabled as the other two get little enough experience in that profession as is.
For now, my nearly 200 breeding animals just mill around my tiny, temporary 13x5 meeting area/dining room. Note that that space is shared with 217 dwarves, heh. They should be tied up within a couple years once my stockpile levels are finished.
Re: Hauling:
I just use general haulers for the most part. For dwarves not dedicated to generalized hauler duties, anyone working with food has everything but food hauling disabled (Food is the only hauling duty I consider to be time sensitive) and the other dwarves typically either have all hauling disabled (Like my four active bonecarvers (One other that's +5 legendary)) that have an endless supply of bones or have all "domestic" (read: safe) hauling jobs enabled if they're a skilled dwarf that has frequent downtime (eg. furnace operators between goblinite deliveries).
For general haulers, of which 35 out of my 217 dwarves are, all hauling jobs are enabled and they have pump operating enabled to both train up their stats and give them legendary status in order to avoid economy issues.